MolNFT v1 · #61419 · protein
Crystal structure of the replication initiator protein encoded on plasmid PMV158 (repb), tetragonal form, to 3.6 ang resolution
3DKY · Replication protein repb: “Crystal structure of the replication initiator protein encoded on plasmid PMV158 (repb), tetragonal form, to…”. X-ray diffraction, 1 ligand (MN), 11 pockets (best druggability 0.73). MolNFT v1 #61419 on…
- PDB
- 3DKY
- Type
- protein
- Length
- 1,161 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication protein repb
- UniProt
- P13921
- Ligands
- MN
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication protein repb | protein | 200 | 47% helix, 17% strand | P13921 |
| B, C | Replication protein repb | protein | 201 | 48% helix, 16% strand | P13921 |
| D | Replication protein repb | protein | 189 | 49% helix, 16% strand | P13921 |
| E | Replication protein repb | protein | 180 | 52% helix, 11% strand | P13921 |
| F | Replication protein repb | protein | 190 | 49% helix, 17% strand | P13921 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.73 | 0.77 | 80 | empty |
| 2 | 1001 | 0.72 | 0.76 | 90 | empty |
| 3 | 541 | 0.64 | 0.76 | 44 | empty |
| 4 | 364 | 0.54 | 0.74 | 30 | empty |
| 5 | 169 | 0.49 | 0.77 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1573 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1550 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1534 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1161 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 952 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3DKY · Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB)… · the same entry in another collection · chain F against F, TM-score 1.00
- P13921 · AlphaFold monomer V2.0 prediction for replication protein repb (P13921) · a predicted model of the same protein · chain B against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P13921
- Elsewhere: RCSB PDB 3DKY · PDBe 3DKY · UniProt P13921
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